6NK5: Electron Cryo-Microscopy Of Chikungunya VLP

Electron Cryo-Microscopy Of Chikungunya VLP. Determined by electron microscopy at 4.16 Å resolution. Released 22 May 2019.

Method: Electron microscopy
Resolution: 4.16 Å
Organism: Chikungunya virus (strain 37997)
Chains: 12
Atoms: 31,130
Mol. weight: 444.42 kDa
Ligands: NAG
Released: 22 May 2019

Explore 6NK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NK5 contains 78 α-helices and 376 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-19	5	2
β-strand	24	1	3
β-strand	27-38	12	2
β-strand	43-48	6	4
β-strand	51-54	4	5
α-helix	57-58	2
β-strand	59-61	3	6
β-strand	77-81	5	6
β-strand	86	1	7
β-strand	88	1	8
β-strand	91	1	8
β-strand	101-106	6	6
β-strand	107-110	4	5
α-helix	113-115	3
β-strand	119-123	5	4
β-strand	130-136	7	2
β-strand	141-147	7	2
β-strand	154-155	2	1
β-strand	160-163	4	1
β-strand	176-180	5	4
β-strand	183-185	3	4
α-helix	195-196	2
β-strand	203-204	2	9
β-strand	205	1	4
β-strand	214-215	2	9
β-strand	221	1	10
β-strand	227	1	7
β-strand	233	1	10
α-helix	234-237	4
α-helix	240-243	4
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-281	7	1
β-strand	289	1	3
β-strand	296-306	11	11
β-strand	307	1	12
β-strand	314-322	9	11
β-strand	326-329	4	13
β-strand	330-332	3	14
β-strand	338-339	2	11
β-strand	343-346	4	13
β-strand	349-357	9	11
β-strand	362-369	8	14
β-strand	373-379	7	14
β-strand	381	1	12
β-strand	387-388	2	15
α-helix	393-395	3
α-helix	406-413	8
α-helix	418-432	15

Chain B: 8 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	32
β-strand	15-20	6	33
β-strand	24	1	34
β-strand	26-31	6	33
β-strand	32-39	8	35
α-helix	40-42	3
β-strand	44-48	5	36
β-strand	52-54	3	37
α-helix	56-58	3
β-strand	59-61	3	38
β-strand	77-82	6	38
β-strand	86	1	39
β-strand	88	1	40
β-strand	91	1	40
β-strand	101-106	6	38
β-strand	107-109	3	37
α-helix	113-116	4
β-strand	119-123	5	36
β-strand	128-136	9	35
β-strand	141-146	6	35
β-strand	153-156	4	32
β-strand	159-163	5	32
β-strand	176-180	5	36
β-strand	183-185	3	36
α-helix	189-191	3
α-helix	195-196	2
β-strand	204-205	2	36
β-strand	214	1	36
β-strand	221	1	41
β-strand	227	1	39
β-strand	233	1	41
β-strand	260-262	3	42
β-strand	267-269	3	42
β-strand	275-281	7	32
α-helix	284-286	3
β-strand	289	1	34
β-strand	296-306	11	43
β-strand	314-322	9	43
β-strand	326-329	4	44
β-strand	330-332	3	45
β-strand	337-339	3	43
β-strand	343-346	4	44
β-strand	351-358	8	43
β-strand	362-369	8	45
β-strand	373-379	7	45
β-strand	387-388	2	46
α-helix	406-413	8
α-helix	418-432	15

Chain C: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	61
β-strand	15-19	5	62
β-strand	24	1	63
β-strand	27-39	13	62
β-strand	43-48	6	64
β-strand	51-54	4	65
α-helix	56-58	3
β-strand	59-61	3	66
β-strand	77-81	5	66
β-strand	88	1	67
β-strand	91	1	67
β-strand	101-106	6	66
β-strand	107-110	4	65
α-helix	112-115	4
β-strand	119-123	5	64
β-strand	128-137	10	62
β-strand	140-147	8	62
β-strand	152	1	68
β-strand	153-156	4	61
β-strand	159-163	5	61
β-strand	176-180	5	64
β-strand	184-186	3	64
β-strand	192	1	69
α-helix	195-196	2
β-strand	204	1	70
β-strand	205	1	64
β-strand	214	1	70
α-helix	223-225	3
α-helix	239-243	5
α-helix	256-258	3
β-strand	260-262	3	62
β-strand	267-269	3	62
β-strand	275-281	7	61
β-strand	289	1	63
α-helix	294-295	2
β-strand	296-302	7	71
β-strand	306	1	71
β-strand	307	1	72
β-strand	314-322	9	71
β-strand	326-329	4	73
β-strand	330-332	3	74
β-strand	338-339	2	71
β-strand	343-346	4	73
β-strand	349-357	9	71
β-strand	362-369	8	74
β-strand	373-379	7	74
β-strand	381	1	72
β-strand	387-388	2	75
α-helix	406-413	8
α-helix	418-431	14
α-helix	432-434	3

Chain D: 10 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	91
β-strand	15-19	5	92
β-strand	24	1	93
β-strand	27-37	11	92
β-strand	38	1	94
β-strand	40-48	9	95
β-strand	51-54	4	96
α-helix	57-58	2
β-strand	59-61	3	97
α-helix	68-70	3
β-strand	77-81	5	97
β-strand	88	1	98
β-strand	91	1	98
β-strand	101-106	6	97
β-strand	107-110	4	96
α-helix	113-115	3
β-strand	119-127	9	95
β-strand	130-136	7	92
β-strand	141-147	7	92
β-strand	149	1	99
β-strand	152	1	69
β-strand	153-156	4	91
β-strand	159-163	5	91
β-strand	165	1	99
β-strand	176-180	5	95
β-strand	183-185	3	95
α-helix	189-191	3
β-strand	192	1	68
α-helix	195-196	2
β-strand	203-204	2	100
β-strand	205	1	95
β-strand	214-215	2	100
β-strand	221	1	101
β-strand	233	1	101
α-helix	240-243	4
α-helix	256-258	3
β-strand	260-262	3	94
β-strand	267-269	3	94
β-strand	275-281	7	91
β-strand	289	1	93
β-strand	297-307	11	102
β-strand	314-321	8	102
β-strand	326-329	4	103
β-strand	330-332	3	104
β-strand	338-339	2	102
β-strand	343-346	4	103
β-strand	349-357	9	102
β-strand	362-369	8	104
β-strand	372-379	8	104
β-strand	380-381	2	102
β-strand	387-388	2	105
α-helix	406-413	8
α-helix	418-431	14
α-helix	432-434	3

Chain E: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	16
β-strand	28-30	3	16
β-strand	36-38	3	17
β-strand	45-49	5	17
β-strand	53-54	2	18
β-strand	66-70	5	18
β-strand	75-79	5	18
α-helix	80-82	3
β-strand	84-86	3	19
β-strand	90	1	19
β-strand	92-97	6	17
β-strand	100-104	5	17
β-strand	110-116	7	19
β-strand	122-128	7	19
α-helix	133-135	3
β-strand	139	1	20
β-strand	148-156	9	21
β-strand	167	1	22
β-strand	169-170	2	23
β-strand	175-176	2	24
β-strand	181-182	2	25
β-strand	188-190	3	25
β-strand	197-201	5	24
β-strand	208-211	4	24
β-strand	215-217	3	25
β-strand	225-229	5	24
β-strand	236-237	2	23
β-strand	255	1	22
β-strand	261-269	9	21
α-helix	270-273	4
β-strand	275-279	5	26
β-strand	282-287	6	26
β-strand	293-299	7	20
β-strand	307-311	5	20
β-strand	315-320	6	26
β-strand	326-330	5	20
β-strand	336-338	3	20
β-strand	339-340	2	15
α-helix	356-361	6
α-helix	368-397	30
α-helix	409-413	5

Chain F: 5 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	47
β-strand	17-19	3	48
β-strand	21	1	49
β-strand	28-30	3	48
β-strand	34-38	5	50
β-strand	45-54	10	50
β-strand	66-70	5	50
β-strand	75-79	5	50
β-strand	84-86	3	49
β-strand	90	1	49
β-strand	92-104	13	50
β-strand	108-116	9	49
β-strand	122-131	10	49
α-helix	133-136	4
β-strand	139	1	51
β-strand	148-156	9	52
β-strand	166-168	3	53
β-strand	169-170	2	54
β-strand	181-183	3	55
β-strand	188-190	3	55
β-strand	197-201	5	56
β-strand	209-211	3	56
β-strand	215-217	3	55
β-strand	225-229	5	56
β-strand	235	1	47
β-strand	236-237	2	54
β-strand	254-256	3	53
β-strand	261-269	9	52
β-strand	275-279	5	57
β-strand	282-287	6	57
β-strand	293-299	7	51
β-strand	307-311	5	51
β-strand	315-320	6	57
β-strand	326-330	5	51
β-strand	336-338	3	51
β-strand	339-340	2	46
α-helix	356-359	4
α-helix	368-397	30
α-helix	398-400	3
α-helix	409-413	5

Chain G: 7 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	76
β-strand	17-19	3	77
β-strand	21	1	78
β-strand	28-30	3	77
β-strand	36-38	3	79
β-strand	46-54	9	79
β-strand	66-70	5	79
β-strand	75-79	5	79
β-strand	84-86	3	78
β-strand	90	1	78
β-strand	92-104	13	79
β-strand	108	1	80
β-strand	111-116	6	78
β-strand	122-127	6	78
β-strand	131	1	80
α-helix	133-135	3
β-strand	139	1	81
β-strand	149-156	8	82
β-strand	166-168	3	83
β-strand	169-170	2	84
β-strand	181-184	4	85
β-strand	187-190	4	85
β-strand	197-201	5	86
β-strand	208-211	4	86
β-strand	215-217	3	85
β-strand	225-229	5	86
β-strand	235	1	76
β-strand	236-237	2	84
α-helix	243-244	2
β-strand	254-256	3	83
β-strand	261-268	8	82
α-helix	269	1
α-helix	272-274	3
β-strand	275-279	5	87
β-strand	282-287	6	87
β-strand	293-299	7	81
β-strand	307-311	5	81
β-strand	315-319	5	87
β-strand	326-330	5	81
α-helix	334-335	2
β-strand	336-338	3	81
β-strand	339-340	2	75
α-helix	358-361	4
α-helix	369-400	32

Chain H: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	17-19	3	106
β-strand	28-30	3	106
β-strand	36-38	3	107
β-strand	45-49	5	107
β-strand	53-54	2	108
β-strand	66-70	5	108
β-strand	75-79	5	108
α-helix	80-82	3
β-strand	84-86	3	109
β-strand	90	1	109
β-strand	92-97	6	107
β-strand	100-104	5	107
β-strand	108-116	9	109
β-strand	122-131	10	109
α-helix	133-135	3
β-strand	136	1	110
β-strand	139	1	110
β-strand	149-156	8	111
β-strand	167	1	112
β-strand	169-170	2	113
β-strand	175-176	2	114
β-strand	182	1	115
β-strand	188-190	3	115
β-strand	197-200	4	114
β-strand	208-210	3	114
β-strand	215-217	3	115
β-strand	227-229	3	114
β-strand	236-237	2	113
α-helix	243-244	2
α-helix	250-251	2
β-strand	255	1	112
β-strand	261-268	8	111
α-helix	272-274	3
β-strand	275-279	5	116
β-strand	282-287	6	116
β-strand	293-298	6	117
β-strand	307-311	5	117
β-strand	315-320	6	116
β-strand	326-330	5	117
α-helix	334-335	2
β-strand	336-338	3	117
β-strand	339-340	2	105
α-helix	358-360	3
α-helix	369-397	29
α-helix	411-414	4

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E1 glycoprotein	A, B, C, D	protein	439	Chikungunya virus (strain 37997)	Q5XXP3
E2 glycoprotein	E, F, G, H	protein	419	Chikungunya virus (strain 37997)	Q5XXP3
Capsid protein	I, J, K, L	protein	151	Chikungunya virus (strain 37997)	Q5XXP3

Sequence of entity 1 (A, B, C, D), FASTA

>6NK5_1 E1 glycoprotein (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTRVVDAPSVTDMS
CEVPACTHSSDFGGVAIIKYTASKKGKCAVHSMTNAVTIREADVEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAACHPPKDHIVNYPASHTTLGVQDISTTAMSWVQKITGGVGLI
VAVAALILIVVLCVSFSRH

Sequence of entity 2 (E, F, G, H), FASTA

>6NK5_2 E2 glycoprotein (chains E, F, G, H)
NFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHT
CTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQ
SGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPR
NAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEP
NYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYP
TMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

Sequence of entity 3 (I, J, K, L), FASTA

>6NK5_3 Capsid protein (chains I, J, K, L)
NDCIFEVKHEGKVMGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVH
MKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLG
GANEGARTALSVVTWNKDIVTKITPEGAEEW

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor. Basore, K., Kim, A.S., Nelson, C.A. et al. Cell (2019) 177:1725. DOI 10.1016/j.cell.2019.04.006 · PubMed

Other PDB entries of the same protein (UniProt Q5XXP3), best resolution first:

9W89 2.89 Å, Chikungunya virus E protein complexed with 10D5
9W8A 2.95 Å, Chikungunya virus E protein complexed with 7H9
9W7J 2.97 Å, Chikungunya virus E protein complexed with 8D1-H-10D5
8DWW 3.13 Å, Chikungunya VLP in complex with neutralizing Fab 506.A08 (asymmetric unit)
8DWY 3.18 Å, Chikungunya VLP in complex with neutralizing Fab CHK-265 (asymmetric unit)
8DWX 3.27 Å, Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)
8EWF 3.92 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the avian…
6NK6 4.06 Å, Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor
3J2W 5.0 Å, Electron cryo-microscopy of Chikungunya virus
5VU2 6.8 Å, Electron cryo-microscopy of "immature" Chikungunya VLP

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